While it worked initially, eventually the clip started to fail and I'd have to wiggle it to get ISP to work. Finally, it died and I had to connect the programmer to pins manually. A fellow freak actually warned this would happen, but alas I tried it anyway to save space.

The Pomona clips are really nice, but they too will wear out quickly (right when you need it most). A setup with pogo-pins will last longer, and if you design it correctly you can replace the pins as they wear out.

I had a board whose thickness was the same as the distance between the rows of a DB9 connector. So I brought the RST,SCK,MISO,MOSI,gnd lines to the edge of the board and made pads that were the same distance apart as the solder cups on the DB9 connector. Then I just pressed the connector onto each board for programming. It worked OK.

The Pomona clips are really nice, but they too will wear out quickly (right when you need it most). A setup with pogo-pins will last longer, and if you design it correctly you can replace the pins as they wear out.

I searched into the forum but I can't find a good setup for an AVR ISP with pogo pins.
Anyway, how they works? I need to push the pins against the board while programming, don't I?

It would be nice if I can leave the connector for some time without hands.

Pogo pins are spring loaded PCB probes that make contact with your DUT (in your case a PCB with AVR). The pogos are inserted into an insulated carrier with a pattern that matches the programming pins on your PCB. Alignment pin holes should be added to your PCB so that the PCB will contact the probes. Your alignment pins will also need a shoulder. This is to establish the proper spring compression onto the pogos when the DUT is placed on the fixture. Usually, there is also some sort of clamp that holds the DUT to the fixture (especially for production fixtures). But, you can hold the board down by hand if your volumes aren't that high. If you don't have room for alignment pins inside the PCB outline, you can also create alignment pins outside the board perimeter, but the positioning won't be quite as accurate.

A link to a 0.050" center to center probe from IDI is shown. There are other sizes of probes and receptacles as well.

I met the inventor, Neil Sherman, at an exhibition in October 2010, when it was being shown as a new product - so it wouldn't have been well-known or widely available at the time of the opening post in this thread.

Often a standard FR4 fiberglass printed circuit board is about 0.1 inch (2.5mm) in thickness. With this thickness, you can use a standard 0.1 inch dual header where the pins are in two rows and use this as a card-edge connector. One row can be on the top side of the board and the other row on the bottom side. On the dual header pin strip, there is usually about 0.2 inches between the tip of the header pin and the black plastic that holds the pins. You could route the ISP traces to the edge of the board, press (but don't solder) a 2x3 or 2x5 header onto these top-and-bottom card-edges for programming, and then remove the header once the AVR has been programmed. The pads can be any size, but their centers need to be spaced 0.1 inches apart.